Contacts of the helix formed by residues 577 - 586 (chain B) in PDB entry 3KUT
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 577 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B HIS* 3.0 25.5 + - + +
576B THR* 1.3 96.1 - - - +
578B ALA* 1.3 65.1 + - - +
579B GLY 3.4 2.5 - - - -
580B LYS* 3.2 9.3 + - + +
581B ILE* 2.9 36.3 + - + +
611B VAL* 4.4 26.7 - - + -
614B LEU* 4.3 20.0 - - + -
615B GLN* 4.8 10.3 - - + +
618B GLN* 5.7 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 578 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567B PHE* 3.5 23.8 - - + -
570B ILE* 4.0 9.7 - - - +
571B GLN* 3.6 31.9 - - + +
574B HIS 3.1 7.4 + - - +
575B PRO 3.8 8.5 + - - +
576B THR 3.6 1.8 - - - -
577B LEU* 1.3 76.0 - - - +
579B GLY* 1.3 58.2 + - - +
582B THR* 2.8 35.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 579 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567B PHE* 3.7 9.6 - - - -
577B LEU 3.4 0.6 - - - -
578B ALA* 1.3 78.1 - - - +
580B LYS* 1.3 57.1 + - - +
582B THR* 4.6 0.4 - - - -
583B GLY 3.0 14.9 + - - -
117D GLU* 3.5 20.3 + - - -
118D PHE* 2.9 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 580 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577B LEU* 3.2 11.8 + - + +
579B GLY* 1.3 73.9 - - - +
581B ILE* 1.3 64.6 + - - +
583B GLY* 3.2 2.3 + - - -
584B MET* 3.0 30.9 + - + +
614B LEU* 3.7 35.4 - - + -
618B GLN* 5.3 3.8 - - - +
113D PRO 3.0 30.0 + - - -
114D ASN* 4.0 4.9 + - - +
115D ALA 2.8 28.9 + - - +
117D GLU* 3.8 20.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 581 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570B ILE* 3.7 22.9 - - + -
574B HIS* 5.2 2.2 - - + -
577B LEU* 2.9 35.0 + - + +
580B LYS* 1.3 71.9 - - - +
582B THR* 1.3 64.3 + - - +
584B MET* 3.2 8.0 + - - +
585B LEU* 2.9 30.0 + - + +
607B VAL* 4.1 16.2 - - + -
610B ALA* 3.8 40.4 - - + +
611B VAL* 3.9 15.0 - - + +
614B LEU* 3.7 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 582 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563B GLY* 4.2 20.4 - - - +
566B LEU* 4.4 8.7 - - + -
567B PHE* 3.7 15.6 - - - +
570B ILE* 3.5 25.9 - - + +
578B ALA 2.8 22.9 + - - -
581B ILE* 1.3 77.2 - - - +
583B GLY* 1.3 57.3 + - - +
585B LEU* 3.2 3.1 + - - +
586B LEU* 2.9 35.7 + - + +
118D PHE* 3.8 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 583 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579B GLY 3.0 12.9 + - - -
580B LYS 3.2 2.9 + - - -
582B THR* 1.3 77.2 - - - +
584B MET* 1.3 61.8 + - - +
586B LEU* 3.4 17.5 + - - +
587B GLU* 3.7 6.9 + - - +
115D ALA* 3.5 14.8 - - - +
116D ALA 3.2 23.0 - - - +
118D PHE* 3.8 8.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 584 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580B LYS* 3.0 23.8 + - + +
581B ILE* 3.5 19.3 - - - +
583B GLY* 1.3 76.2 - - - +
585B LEU* 1.3 63.2 + - + +
587B GLU* 3.3 17.8 + - - +
588B ILE 4.3 0.5 + - - -
610B ALA* 3.6 33.9 - - + +
613B VAL* 4.2 8.1 - - + -
614B LEU* 4.0 21.1 - - - +
111D LEU* 3.7 25.7 - - + +
112D ASN 3.3 20.4 + - - +
113D PRO* 3.8 29.4 - - + -
115D ALA* 3.6 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 585 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566B LEU* 5.1 4.5 - - + -
570B ILE* 4.0 15.0 - - + -
581B ILE* 2.9 26.4 + - + +
582B THR 3.8 3.8 - - - +
584B MET* 1.3 76.7 - - - +
586B LEU* 1.3 62.3 + - - +
587B GLU 3.1 0.2 - - - -
588B ILE* 3.0 28.9 + - + +
593B LEU* 3.4 10.3 - - + +
596B MET* 4.1 9.0 - - + -
603B LEU* 3.6 30.7 - - + -
606B LYS* 3.8 33.9 - - + +
607B VAL* 4.0 6.3 - - + -
610B ALA* 3.8 26.0 - - + -
111D LEU* 4.2 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 586 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559B LYS* 2.8 67.9 + - + +
562B LEU* 4.1 11.2 - - + -
563B GLY* 3.6 17.5 - - - +
566B LEU* 4.1 10.5 - - + -
582B THR* 2.9 23.0 + - + +
583B GLY* 3.7 8.3 - - - +
584B MET 3.2 0.6 - - - -
585B LEU* 1.3 74.6 - - - +
587B GLU* 1.3 57.9 + - - +
588B ILE 3.2 1.1 - - - -
593B LEU* 4.1 8.1 - - + -
118D PHE* 3.5 36.3 - - + -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il